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Kuciński M, Jakubowska-Lehrmann M, Góra A, Mirny Z, Nadolna-Ałtyn K, Szlinder-Richert J, Ocalewicz K. Population Genetic Study on the European Flounder ( Platichthys flesus) from the Southern Baltic Sea Using SNPs and Microsatellite Markers. Animals (Basel) 2023; 13:ani13091448. [PMID: 37174485 PMCID: PMC10177365 DOI: 10.3390/ani13091448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/14/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
The European flounder (Platichthys flesus), which is closely related to the recently discovered Baltic flounder (Platichthys solemdali), is currently the third most commercially fished species in the Baltic Sea. According to the available data from the Polish Fisheries Monitoring Center and fishermen's observations, the body condition indices of the species in the Baltic Sea have declined in recent years. The aim of the present study was to obtain information on the current patterns of genetic variability and the population structure of the European flounder and to verify whether the Baltic flounder is present in the southern Baltic Sea. Moreover, we aimed to verify whether the observed decline in the body condition indices of the species in the Baltic Sea might be associated with adaptive alterations in its gene pool due to increased fishing pressure. For this purpose, 190 fish were collected from four locations along the central coastline of Poland, i.e., Mechelinki, Władysławowo, the Vistula Lagoon in 2018, and the Słupsk Bank in 2020. The fish were morphologically analyzed and then genetically screened by the application of nineteen microsatellite DNA and two diagnostic SNP markers. The examined European flounder specimens displayed a high level of genetic diversity (PIC = 0.832-0.903, I = 2.579-2.768). A lack of significant genetic differentiation (Fst = 0.004, p > 0.05) was observed in all the examined fish, indicating that the European flounder in the sampled area constitutes a single genetic cluster. A significant deficiency in heterozygotes (Fis = 0.093, p < 0.05) and overall deviations from Hardy-Weinberg expectations (H-WE) were only detected in fish sampled from the Słupsk Bank. The estimated effective population size (Ne) among the sampled fish groups varied from 712 (Słupsk Bank) to 10,115 (Władysławowo and Mechelinki). However, the recorded values of the Garza-Williamson indicator (M = 0.574-0.600) and the lack of significant (p > 0.05) differences in Heq > He under the SMM model did not support the species' population size changes in the past. The applied SNP markers did not detect the presence of the Baltic flounder among the fish sampled from the studied area. The analysis of an association between biological traits and patterns of genetic diversity did not detect any signs of directional selection or density-dependent adaptive changes in the gene pool of the examined fish that might be caused by increased fishing pressure.
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Affiliation(s)
- Marcin Kuciński
- Department of Marine Biology and Ecology, Institute of Oceanography, University of Gdansk, Piłsudskiego Ave. 46, 81-378 Gdynia, Poland
| | - Magdalena Jakubowska-Lehrmann
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, Kołłątaja 1 Street, 81-332 Gdynia, Poland
| | - Agnieszka Góra
- Department of Food and Environmental Chemistry, National Marine Fisheries Research Institute, Kołłątaja 1 Street, 81-332 Gdynia, Poland
| | - Zuzanna Mirny
- Department of Fisheries Resources, National Marine Fisheries Research Institute, Kołłątaja 1 Street, 81-332 Gdynia, Poland
| | - Katarzyna Nadolna-Ałtyn
- Department of Fisheries Resources, National Marine Fisheries Research Institute, Kołłątaja 1 Street, 81-332 Gdynia, Poland
| | - Joanna Szlinder-Richert
- Department of Food and Environmental Chemistry, National Marine Fisheries Research Institute, Kołłątaja 1 Street, 81-332 Gdynia, Poland
| | - Konrad Ocalewicz
- Department of Marine Biology and Ecology, Institute of Oceanography, University of Gdansk, Piłsudskiego Ave. 46, 81-378 Gdynia, Poland
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Klein JD, der Merwe AEBV, Dicken ML, Emami-Khoyi A, Mmonwa KL, Teske PR. A globally threatened shark, Carcharias taurus, shows no population decline in South Africa. Sci Rep 2020; 10:17959. [PMID: 33087802 PMCID: PMC7578018 DOI: 10.1038/s41598-020-75044-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/09/2020] [Indexed: 12/03/2022] Open
Abstract
Knowledge about the demographic histories of natural populations helps to evaluate their conservation status, and potential impacts of natural and anthropogenic pressures. In particular, estimates of effective population size obtained through molecular data can provide useful information to guide management decisions for vulnerable populations. The spotted ragged-tooth shark, Carcharias taurus (also known as the sandtiger or grey nurse shark), is widely distributed in warm-temperate and subtropical waters, but has suffered severe population declines across much of its range as a result of overexploitation. Here, we used multilocus genotype data to investigate the demographic history of the South African C. taurus population. Using approximate Bayesian computation and likelihood-based importance sampling, we found that the population underwent a historical range expansion that may have been linked to climatic changes during the late Pleistocene. There was no evidence for a recent anthropogenic decline. Together with census data suggesting a stable population, these results support the idea that fishing pressure and other threats have so far not been detrimental to the local C. taurus population. The results reported here indicate that South Africa could possibly harbour the last remaining, relatively pristine population of this widespread but vulnerable top predator.
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Affiliation(s)
- Juliana D Klein
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Aletta E Bester-van der Merwe
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Matthew L Dicken
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, 4320, South Africa
- Department of Development Studies, School of Economics, Development and Tourism, Nelson Mandela University, Port Elizabeth, 6031, South Africa
| | - Arsalan Emami-Khoyi
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Kolobe L Mmonwa
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, 4320, South Africa
| | - Peter R Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa.
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Abstract
Natural highly fecund populations abound. These range from viruses to gadids. Many highly fecund populations are economically important. Highly fecund populations provide an important contrast to the low-fecundity organisms that have traditionally been applied in evolutionary studies. A key question regarding high fecundity is whether large numbers of offspring are produced on a regular basis, by few individuals each time, in a sweepstakes mode of reproduction. Such reproduction characteristics are not incorporated into the classical Wright-Fisher model, the standard reference model of population genetics, or similar types of models, in which each individual can produce only small numbers of offspring relative to the population size. The expected genomic footprints of population genetic models of sweepstakes reproduction are very different from those of the Wright-Fisher model. A key, immediate issue involves identifying the footprints of sweepstakes reproduction in genomic data. Whole-genome sequencing data can be used to distinguish the patterns made by sweepstakes reproduction from the patterns made by population growth in a population evolving according to the Wright-Fisher model (or similar models). If the hypothesis of sweepstakes reproduction cannot be rejected, then models of sweepstakes reproduction and associated multiple-merger coalescents will become at least as relevant as the Wright-Fisher model (or similar models) and the Kingman coalescent, the cornerstones of mathematical population genetics, in further discussions of evolutionary genomics of highly fecund populations.
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Affiliation(s)
- Bjarki Eldon
- Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, D-10115 Berlin, Germany;
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Righi T, Splendiani A, Fioravanti T, Petetta A, Candelma M, Gioacchini G, Gillespie K, Hanke A, Carnevali O, Caputo Barucchi V. Mediterranean swordfish ( Xiphias gladius Linnaeus, 1758) population structure revealed by microsatellite DNA: genetic diversity masked by population mixing in shared areas. PeerJ 2020; 8:e9518. [PMID: 33194325 PMCID: PMC7394060 DOI: 10.7717/peerj.9518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 06/19/2020] [Indexed: 11/20/2022] Open
Abstract
Background The Mediterranean swordfish stock is overfished and considered not correctly managed. Elucidating the patterns of the Mediterranean swordfish population structure constitutes an essential prerequisite for effective management of this fishery resource. To date, few studies have investigated intra-Mediterranean swordfish population structure, and their conclusions are controversial. Methods A panel of 20 microsatellites DNA was used to investigate fine-scale population structuring of swordfish from six main fishing areas of the Mediterranean Sea. Results This study provides evidence to reject the hypothesis of a single swordfish population within the Mediterranean Sea. DAPC analysis revealed the presence of three genetic clusters and a high level of admixture within the Mediterranean Sea. Genetic structure was supported by significant FST values while mixing was endorsed by the heterozygosity deficit observed in sampling localities indicative of a possible Wahlund effect, by sampling admixture individuals. Overall, our tests reject the hypothesis of a single swordfish population within the Mediterranean Sea. Homing towards the Mediterranean breeding areas may have generated a weak degree of genetic differentiation between populations even at the intra-basin scale.
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Affiliation(s)
- Tommaso Righi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Andrea Splendiani
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Tatiana Fioravanti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Andrea Petetta
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Michela Candelma
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Giorgia Gioacchini
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Kyle Gillespie
- Fisheries and Oceans Canada, St. Andrews Biological Station, Ottawa, Canada
| | - Alex Hanke
- Fisheries and Oceans Canada, St. Andrews Biological Station, Ottawa, Canada
| | - Oliana Carnevali
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Vincenzo Caputo Barucchi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
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Loss of Mitochondrial Genetic Diversity in Overexploited Mediterranean Swordfish (Xiphias gladius, 1759) Population. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12050170] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Intense and prolonged mortality caused by over-exploitation could drive the decay of genetic diversity which may lead to decrease species’ resilience to environmental changes, thus increasing their extinction risk. Swordfish is a high commercial value species, especially in the Mediterranean Sea, where it is affected by high catch levels. Mediterranean swordfish consist of a population genetically and biologically distinct from Atlantic ones and therefore managed as a separate stock. The last Mediterranean swordfish stock assessment reported that in the last forty years Mediterranean swordfish has been overfished and, to date, it is still subject to overfishing. A comparison between an available mitochondrial sequence dataset and a homologous current sample was carried out to investigate temporal genetic variation in the Mediterranean swordfish population over near twenty years. Our study provides the first direct measure of reduced genetic diversity for Mediterranean swordfish during a short period, as measured both in the direct loss of mitochondrial haplotypes and reduction in haplotype diversity. A reduction of the relative females’ effective population size in the recent sample has been also detected. The possible relationship between fishery activities and the loss of genetic diversity in the Mediterranean swordfish population is discussed.
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Miccoli A, Maradonna F, De Felice A, Caputo Barucchi V, Estonba A, Genangeli M, Vittori S, Leonori I, Carnevali O. Detection of endocrine disrupting chemicals and evidence of their effects on the HPG axis of the European anchovy Engraulis encrasicolus. MARINE ENVIRONMENTAL RESEARCH 2017; 127:137-147. [PMID: 28411869 DOI: 10.1016/j.marenvres.2017.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
Natural/synthetic Endocrine Disrupting Chemicals (EDCs) may display estrogenic activity and a lower potency than 17β-estradiol. Nonetheless, their concentrations and additive effects can affect the endocrine system and reproductive processes related to the Hypothalamic-Pituitary-Gonadal (HPG) axis. Because of their persistence in both the environment and biological systems, they ultimately target multi-level predators, including humans. We detected presence and effects of xenobiotics on wild anchovy Engraulis encrasicolus in the Western Adriatic Sea. Twenty-one PCBs and five organochlorines were detected on the order of ng g-1; vitellogenin, vitellogenin receptor and genes encoding for the zona radiata proteins were evaluated in gonad and/or liver and found transcribed in male specimens; in addition, intersex was histologically identified in the 13% of testis. Our results have developed the understanding of the European anchovy's reproductive toxicological risk and our approach could assist the comprehension of the complex dynamics of commercially relevant Teleost species.
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Affiliation(s)
- Andrea Miccoli
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy; CNR-National Research Council of Italy, ISMAR-Marine Sciences Institute, Ancona, Italy.
| | - Francesca Maradonna
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy.
| | - Andrea De Felice
- CNR-National Research Council of Italy, ISMAR-Marine Sciences Institute, Ancona, Italy.
| | - Vincenzo Caputo Barucchi
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy.
| | - Andone Estonba
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain.
| | | | - Sauro Vittori
- School of Pharmacy, University of Camerino, Camerino, Italy.
| | - Iole Leonori
- CNR-National Research Council of Italy, ISMAR-Marine Sciences Institute, Ancona, Italy.
| | - Oliana Carnevali
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy.
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Ovenden JR, Leigh GM, Blower DC, Jones AT, Moore A, Bustamante C, Buckworth RC, Bennett MB, Dudgeon CL. Can estimates of genetic effective population size contribute to fisheries stock assessments? JOURNAL OF FISH BIOLOGY 2016; 89:2505-2518. [PMID: 27730623 DOI: 10.1111/jfb.13129] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/28/2016] [Indexed: 06/06/2023]
Abstract
Sustainable exploitation of fisheries populations is challenging to achieve when the size of the population prior to exploitation and the actual numbers removed over time and across fishing zones are not clearly known. Quantitative fisheries' modeling is able to address this problem, but accurate and reliable model outcomes depend on high quality input data. Much of this information is obtained through the operation of the fishery under consideration, but while this seems appropriate, biases may occur. For example, poorly quantified changes in fishing methods that increase catch rates can erroneously suggest that the overall population size is increasing. Hence, the incorporation of estimates of abundance derived from independent data sources is preferable. We review and evaluate a fisheries-independent method of indexing population size; inferring adult abundance from estimates of the genetic effective size of a population (Ne ). Recent studies of elasmobranch species have shown correspondence between Ne and ecologically determined estimates of the population size (N). Simulation studies have flagged the possibility that the range of Ne /N ratios across species may be more restricted than previously thought, and also show that declines in Ne track declines in the abundance of model fisheries species. These key developments bring this new technology closer to implementation in fisheries science, particularly for data-poor fisheries or species of conservation interest.
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Affiliation(s)
- J R Ovenden
- Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - G M Leigh
- Agri-Science Queensland, Department of Agriculture & Fisheries, St Lucia, QLD, 4072, Australia
| | - D C Blower
- Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
- School of Biological Sciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - A T Jones
- Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
- Centre for Applications in Natural Resource Mathematics, School of Mathematics and Physics, University of Queensland, St Lucia, QLD, 4072, Australia
| | - A Moore
- Fisheries, Forestry & Land, Australian Bureau of Agricultural & Resource Economics and Sciences, Department of Agriculture & Water Resources, Canberra, ACT, 2601, Australia
| | - C Bustamante
- Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
- Shark & Ray Research Group, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - R C Buckworth
- Tropical Ecosystems Research Centre, Oceans & Atmosphere, CSIRO, Berrimah, NT, 0820, Australia
| | - M B Bennett
- Shark & Ray Research Group, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - C L Dudgeon
- Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
- Shark & Ray Research Group, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
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Biocomplexity in Populations of European Anchovy in the Adriatic Sea. PLoS One 2016; 11:e0153061. [PMID: 27074008 PMCID: PMC4830579 DOI: 10.1371/journal.pone.0153061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/23/2016] [Indexed: 01/22/2023] Open
Abstract
The sustained exploitation of marine populations requires an understanding of a species' adaptive seascape so that populations can track environmental changes from short- and long-term climate cycles and from human development. The analysis of the distributions of genetic markers among populations, together with correlates of life-history and environmental variability, can provide insights into the extent of adaptive variation. Here, we examined genetic variability among populations of mature European anchovies (n = 531) in the Adriatic (13 samples) and Tyrrhenian seas (2 samples) with neutral and putative non-neutral microsatellite loci. These genetic markers failed to confirm the occurrence of two anchovy species in the Adriatic Sea, as previously postulated. However, we found fine-scale population structure in the Adriatic, especially in northern areas, that was associated with four of the 13 environmental variables tested. Geographic gradients in sea temperature, salinity and dissolved oxygen appear to drive adaptive differences in spawning time and early larval development among populations. Resolving adaptive seascapes in Adriatic anchovies provides a means to understand mechanisms underpinning local adaptation and a basis for optimizing exploitation strategies for sustainable harvests.
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